Science Enabled by Specimen Data

Mu, C., and P. Li. 2023. Assessing the invasion risk of Chelydra serpentina in China under current and future climate change scenarios. Frontiers in Ecology and Evolution 11.

Chelydra serpentina, a species introduced to China for aquaculture purposes, is commonly found in its natural habitats within the country. The invasion of C. serpentina poses potential threats to both the biodiversity of China and human health. The potential distribution of C. serpentina has been simulated using the species distribution model – MaxEnt, incorporating global distribution data, climate, and land cover variables. Our simulations encompasses both current conditions and four future climate change scenarios. Currently, the potential distribution is concentrated in central, eastern, and southeastern regions of China, with the central and eastern regions facing the highest risk of invasion. Under future climate change scenarios, the distribution area may expand by 30–90%, and multiple provinces will face a more severe threat of invasion. This study presents the inaugural simulation of the potential invasion range of C. serpentina under current climatic conditions. Moreover, it reveals that climate change is likely to contribute to the expansion of its invasive range, thus furnishing a reference foundation for scientific prevention and control measures. We propose integrating citizen science and eDNA technologies into species monitoring to enhance the efficiency of detecting invasive species. This research has filled the gap in the research on the invasive distribution range of C. serpentina in China and globally, while also providing novel perspectives on the invasion control of this species.

Groh, S. S., P. Upchurch, J. J. Day, and P. M. Barrett. 2023. The biogeographic history of neosuchian crocodiles and the impact of saltwater tolerance variability. Royal Society Open Science 10.

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

Leão, C. F., M. S. Lima Ribeiro, K. Moraes, G. S. R. Gonçalves, and M. G. M. Lima. 2023. Climate change and carnivores: shifts in the distribution and effectiveness of protected areas in the Amazon. PeerJ 11: e15887.

Background Carnivore mammals are animals vulnerable to human interference, such as climate change and deforestation. Their distribution and persistence are affected by such impacts, mainly in tropical regions such as the Amazon. Due to the importance of carnivores in the maintenance and functioning of the ecosystem, they are extremely important animals for conservation. We evaluated the impact of climate change on the geographic distribution of carnivores in the Amazon using Species Distribution Models (SDMs). Do we seek to answer the following questions: (1) What is the effect of climate change on the distribution of carnivores in the Amazon? (2) Will carnivore species lose or gain representation within the Protected Areas (PAs) of the Amazon in the future? Methods We evaluated the distribution area of 16 species of carnivores mammals in the Amazon, based on two future climate scenarios (RCP 4.5 and RCP 8.5) for the year 2070. For the construction of the SDMs we used bioclimatic and vegetation cover variables (land type). Based on these models, we calculated the area loss and climate suitability of the species, as well as the effectiveness of the protected areas inserted in the Amazon. We estimated the effectiveness of PAs on the individual persistence of carnivores in the future, for this, we used the SDMs to perform the gap analysis. Finally, we analyze the effectiveness of PAs in protecting taxonomic richness in future scenarios. Results The SDMs showed satisfactory predictive performance, with Jaccard values above 0.85 and AUC above 0.91 for all species. In the present and for the future climate scenarios, we observe a reduction of potencial distribution in both future scenarios (RCP4.5 and RCP8.5), where five species will be negatively affected by climate change in the RCP 4.5 future scenario and eight in the RCP 8.5 scenario. The remaining species stay stable in terms of total area. All species in the study showed a loss of climatic suitability. Some species lost almost all climatic suitability in the RCP 8.5 scenario. According to the GAP analysis, all species are protected within the PAs both in the current scenario and in both future climate scenarios. From the null models, we found that in all climate scenarios, the PAs are not efficient in protecting species richness.

Hope, A. G., K. M. Headlee, Z. H. Olson, and B. J. Wiens. 2023. Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change. Systematics and Biodiversity 21.

Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5939 and 11 513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We (1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, (2) test the validity of multiple sub-species designations, (3) provide spatial and temporal historical biogeographic perspectives, and (4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however, nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting the interpretation of ongoing evolutionary processes, particularly in southern portions of the species’ range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.

Cruz, J. A., J. A. Velasco, J. Arroyo-Cabrales, and E. Johnson. 2023. Paleoclimatic Reconstruction Based on the Late Pleistocene San Josecito Cave Stratum 720 Fauna Using Fossil Mammals, Reptiles, and Birds. Diversity 15: 881.

Advances in technology have equipped paleobiologists with new analytical tools to assess the fossil record. The functional traits of vertebrates have been used to infer paleoenvironmental conditions. In Quaternary deposits, birds are the second-most-studied group after mammals. They are considered a poor paleoambiental proxy because their high vagility and phenotypic plasticity allow them to respond more effectively to climate change. Investigating multiple groups is important, but it is not often attempted. Biogeographical and climatic niche information concerning small mammals, reptiles, and birds have been used to infer the paleoclimatic conditions present during the Late Pleistocene at San Josecito Cave (~28,000 14C years BP), Mexico. Warmer and dryer conditions are inferred with respect to the present. The use of all of the groups of small vertebrates is recommended because they represent an assemblage of species that have gone through a series of environmental filters in the past. Individually, different vertebrate groups provide different paleoclimatic information. Birds are a good proxy for inferring paleoprecipitation but not paleotemperature. Together, reptiles and small mammals are a good proxy for inferring paleoprecipitation and paleotemperature, but reptiles alone are a bad proxy, and mammals alone are a good proxy for inferring paleotemperature and precipitation. The current paleoclimatic results coupled with those of a previous vegetation structure analysis indicate the presence of non-analog paleoenvironmental conditions during the Late Pleistocene in the San Josecito Cave area. This situation would explain the presence of a disharmonious fauna and the extinction of several taxa when these conditions later disappeared and do not reappear again.

Fell, H. G., M. Jones, S. Atkinson, N. C. Stenseth, and A. C. Algar. 2023. The role of reservoir species in mediating plague’s dynamic response to climate. Royal Society Open Science 10.

The distribution and transmission of Yersinia pestis , the bacterial agent of plague, responds dynamically to climate, both within wildlife reservoirs and human populations. The exact mechanisms mediating plague's response to climate are still poorly understood, particularly across large environmentally heterogeneous regions encompassing several reservoir species. A heterogeneous response to precipitation was observed in plague intensity across northern and southern China during the Third Pandemic. This has been attributed to the response of reservoir species in each region. We use environmental niche modelling and hindcasting methods to test the response of a broad range of reservoir species to precipitation. We find little support for the hypothesis that the response of reservoir species to precipitation mediated the impact of precipitation on plague intensity. We instead observed that precipitation variables were of limited importance in defining species niches and rarely showed the expected response to precipitation across northern and southern China. These findings do not suggest that precipitation–reservoir species dynamics never influence plague intensity but that instead, the response of reservoir species to precipitation across a single biome cannot be assumed and that limited numbers of reservoir species may have a disproportional impact upon plague intensity.

Ecke, F., B. A. Han, B. Hörnfeldt, H. Khalil, M. Magnusson, N. J. Singh, and R. S. Ostfeld. 2022. Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses. Nature Communications 13.

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species’ synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world. Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.

Moreno, I., J. M. W. Gippet, L. Fumagalli, and P. J. Stephenson. 2022. Factors affecting the availability of data on East African wildlife: the monitoring needs of conservationists are not being met. Biodiversity and Conservation.

Understanding the status and abundance of species is essential for effective conservation decision-making. However, the availability of species data varies across space, taxonomic groups and data types. A case study was therefore conducted in a high biodiversity region—East Africa—to evaluate data biases, the factors influencing data availability, and the consequences for conservation. In each of the eleven target countries, priority animal species were identified as threatened species that are protected by national governments, international conventions or conservation NGOs. We assessed data gaps and biases in the IUCN Red List of Threatened Species, the Global Biodiversity Information Facility and the Living Planet Index. A survey of practitioners and decision makers was conducted to confirm and assess consequences of these biases on biodiversity conservation efforts. Our results showed data on species occurrence and population trends were available for a significantly higher proportion of vertebrates than invertebrates. We observed a geographical bias, with higher tourism income countries having more priority species and more species with data than lower tourism income countries. Conservationists surveyed felt that, of the 40 types of data investigated, those data that are most important to conservation projects are the most difficult to access. The main challenges to data accessibility are excessive expense, technological challenges, and a lack of resources to process and analyse data. With this information, practitioners and decision makers can prioritise how and where to fill gaps to improve data availability and use, and ensure biodiversity monitoring is improved and conservation impacts enhanced.

Rahman, D. A., Y. Santosa, I. Purnamasari, and A. A. Condro. 2022. Drivers of Three Most Charismatic Mammalian Species Distribution across a Multiple-Use Tropical Forest Landscape of Sumatra, Indonesia. Animals 12: 2722.

Tropical Rainforest Heritage sites of Sumatra are some of the most irreplaceable landscapes in the world for biodiversity conservation. These landscapes harbor many endangered Asiatic mammals all suffering multifaceted threats due to anthropogenic activities. Three charismatic mammals in Sumatra: Elephas maximus sumatranus, Pongo abelii, and Panthera tigris sumatrae are protected and listed as Critically Endangered (CR) within the IUCN Red List. Nevertheless, their current geographic distribution remains unclear, and the impact of environmental factors on these species are mostly unknown. This study predicts the potential range of those species on the island of Sumatra using anthropogenic, biophysical, topographic, and climatic parameters based on the ensemble machine learning algorithms. We also investigated the effects of habitat loss from current land use, ecosystem availability, and importance of Indonesian protected areas. Our predictive model had relatively excellent performance (Sørensen: 0.81–0.94) and can enhance knowledge on the current species distributions. The most critical environmental predictors for the distribution of the three species are conservation status and temperature seasonality. This study revealed that more than half of the species distributions occurred in non-protected areas, with proportional coverage being 83%, 72%, and 54% for E.m. sumatranus, P. abelii, and P.t. sumatrae, respectively. Our study further provides reliable information on places where conservation efforts must be prioritized, both inside and outside of the protected area networks, to safeguard the ongoing survival of these Indonesian large charismatic mammals.

González-Bernal, A., O. Rojas-Soto, and E. Martínez-Meyer. 2022. Climatic comparison of the gray wolf (Canis lupus) subspecies in North America using niche-based distribution models and its implications for conservation programs D. Ge [ed.],. Journal of Mammalogy.

Abstract The gray wolf, Canis lupus, once inhabited much of the northern hemisphere worldwide; however, persecution drove its populations almost to extinction. In North America, diverse conservation programs have been implemented in the last decades to recover its populations in the wild, many of them guided by the historical distribution of the gray wolf subspecies. Over time, several authors have proposed different subspecies classifications. Nevertheless, most of them are mutually inconsistent regarding the number and distribution of subspecies, creating controversy when implementing conservation programs. This study used niche-based distribution models and cluster analysis to explore the bioclimatic profiles of C. lupus across North America and compare them with different subspecies classifications to identify environmental correlatives that support the proposed designations. Our cluster analysis results indicate that the optimal number of climatic groups was five, designated as Northern, Eastern, Western, Coastal, and Southern groups, with transitional overlap boundaries located at their peripheries, indicating climatic gradients between them and supporting the idea of intergrading zones. The geographic ranges of these groups mismatched to a different extent with all subspecies delimitations. In general, the boundaries of putative subspecies did not match the climatic patterns of North America. Our results may contribute to the recovery programs underway for this carnivore by identifying suitable areas for the release of individuals from specific lineages. New approaches to characterizing the intraspecific variation of the gray wolf should include all evidence available, including genetic, morphological, and ecological information.